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Interestingly, many of these gene products [https://en.wikipedia.org/wiki/Allobarbital allobarbital] are located in the outer cell envelope (Figure?2D), a selective permeability barrier for Gram-negative bacteria that is severely underrepresented for known essential genes (Figure?2D). Many of the stresses generating CE phenotypes are part of the natural environment of E.?coli, e.g., bile salts ( Table S5), indicating that these genes are likely indispensable for E.?coli to survive in?vivo. Similarly, using the largest metagenomic data set to date, Qin et?al. reported that envelope-specific functions, such as adhesion, were commonly required for life in the gut ( Qin et?al., 2010). A key motivation for our study was to provide phenotypes for mutants of genes without functional annotation. Using a recently assembled compendium of such ��orphan genes�� in E.?coli ( Hu et?al., 2009), we find that the fraction of mutant orphan genes with phenotypes is close to that of annotated genes ( Figure?3A), but the former tend to have fewer phenotypes, indicating the power of phenomic analysis for identifying their phenotypes. Importantly, the phenotypic profiles of > 25% of all orphan genes correlate strongly with those of annotated genes (r �� 0.5; Figure?3B and Table S6), providing high-confidence leads (p?[http://www.selleckchem.com/JNK.html Selleck JNK inhibitor] will be of broad utility. A small fraction of orphan gene knockouts have many phenotypes. Whereas annotated genes that are responsible for many phenotypes are broadly distributed among bacteria, the most responsive orphans tend to be narrowly distributed (Figure?3D). This result suggests that evolutionary conservation is not?a reliable indicator of the importance of an orphan gene to the organism and that annotating them solely by homology has limitations. Such orphans may have evolved to fulfill an important but specialized function required by the niche of the organism. In support of this idea, a multiresponsive orphan identified in this study (lpoB) is restricted to enterobacteria and regulates peptidoglycan synthesis, [http://www.selleckchem.com/products/azd2014.html Selleck AZD2014] a conserved process that is ubiquitous among bacteria ( Typas et?al., 2010). Both correlated phenotypic signatures (Figures 1C and 1D; Typas et?al., 2010) and anticorrelated phenotypic signatures have functional significance. For example, the phenotypic signatures of deletions of a transcriptional repressor and important target genes are likely to be anticorrelated. We find that marR? and marB? were highly anticorrelated with acrB?, whereas marR? and marB? were highly correlated ( Figure?4A). marB is a gene of unknown function in the multiple antibiotic resistance operon (marRAB), which also includes the operon repressor marR and its activator, marA. MarA also activates genes involved in antibiotic resistance, most importantly acrAB, encoding the major antibiotic efflux pump in E.?coli ( Figure?4B) ( Martin and Rosner, 2002).